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commit: 3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 |
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Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> |
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AuthorDate: Thu May 30 11:14:56 2019 +0000 |
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Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> |
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CommitDate: Thu May 30 11:14:56 2019 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e2a2a3b |
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|
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sci-chemistry/vmd: Multiple fixes and update ebuild |
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|
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- Longer explanation to download sources files (#640440) |
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- Fix tachyon support (#644122) |
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- Install netcdf plugin (#661636) |
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|
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Bug: https://bugs.gentoo.org/640440 |
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Closes: https://bugs.gentoo.org/644122 |
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Closes: https://bugs.gentoo.org/661636 |
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Package-Manager: Portage-2.3.66, Repoman-2.3.12 |
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Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> |
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|
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.../vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 8 +- |
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.../vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 + |
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sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 262 +++++++++++++++++++++ |
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3 files changed, 279 insertions(+), 4 deletions(-) |
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|
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diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch |
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index ce842448dec..67eb11bbd36 100644 |
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--- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch |
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+++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch |
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@@ -4,8 +4,8 @@ |
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|
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diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu |
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index 5bfe7bf..36faaf0 100755 |
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---- a/vmd-1.9.1/src/CUDAMarchingCubes.cu |
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-+++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu |
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+--- a/src/CUDAMarchingCubes.cu |
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++++ b/src/CUDAMarchingCubes.cu |
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@@ -45,6 +45,7 @@ |
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#include "CUDAMarchingCubes.h" |
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#include <thrust/scan.h> |
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@@ -16,8 +16,8 @@ index 5bfe7bf..36faaf0 100755 |
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// (limited by shared memory size) |
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diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu |
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index a21ebde..56a42c8 100755 |
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---- a/vmd-1.9.1/src/CUDAQuickSurf.cu |
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-+++ b/vmd-1.9.1/src/CUDAQuickSurf.cu |
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+--- a/src/CUDAQuickSurf.cu |
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++++ b/src/CUDAQuickSurf.cu |
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@@ -22,6 +22,7 @@ |
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#include <stdlib.h> |
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#include <string.h> |
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|
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diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch |
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new file mode 100644 |
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index 00000000000..b71cd97210a |
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--- /dev/null |
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+++ b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch |
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@@ -0,0 +1,13 @@ |
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+--- a/configure.old 2019-05-16 17:26:05.347560700 +0200 |
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++++ b/configure 2019-05-16 17:30:25.478455770 +0200 |
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+@@ -1105,8 +1105,8 @@ |
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+ # This may be commented out if not required. |
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+ $libtachyon_defines = "-DVMDLIBTACHYON"; |
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+ $libtachyon_dir = "$vmd_library_dir/tachyon"; |
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+-$libtachyon_include = "-I$libtachyon_dir/include"; |
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+-$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; |
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++$libtachyon_include = "-Igentoo-libtachyon-include"; |
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++$libtachyon_library = "-Lgentoo-libtachyon-libs"; |
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+ $libtachyon_libs = "-ltachyon"; |
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+ @libtachyon_cc = (); |
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+ @libtachyon_cu = (); |
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|
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diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild |
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new file mode 100644 |
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index 00000000000..392e380ece1 |
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--- /dev/null |
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+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild |
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@@ -0,0 +1,262 @@ |
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+# Copyright 1999-2019 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+PYTHON_COMPAT=( python2_7 ) |
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+ |
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+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs |
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+ |
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+DESCRIPTION="Visual Molecular Dynamics" |
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+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" |
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+SRC_URI=" |
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+ https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz |
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+ ${P}.src.tar |
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+" |
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+ |
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+SLOT="0" |
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+LICENSE="vmd" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+IUSE="cuda gromacs msms povray sqlite tachyon xinerama" |
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+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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+ |
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+RESTRICT="fetch" |
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+ |
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+# currently, tk-8.5* with USE=truetype breaks some |
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+# tk apps such as Sequence Viewer or Timeline. |
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+CDEPEND=" |
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+ >=dev-lang/tk-8.6.1:0= |
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+ dev-lang/perl |
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+ dev-libs/expat |
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+ dev-python/numpy[${PYTHON_USEDEP}] |
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+ sci-libs/netcdf:0= |
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+ virtual/opengl |
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+ >=x11-libs/fltk-1.1.10-r2:1 |
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+ x11-libs/libXft |
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+ x11-libs/libXi |
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+ ${PYTHON_DEPS} |
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+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) |
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+ gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) |
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+ sqlite? ( dev-db/sqlite:3= ) |
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+ tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) |
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+ xinerama? ( x11-libs/libXinerama ) |
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+" |
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+DEPEND="${CDEPEND}" |
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+BDEPEND=" |
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+ virtual/pkgconfig |
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+ dev-lang/swig |
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+" |
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+RDEPEND="${CDEPEND} |
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+ sci-biology/stride |
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+ sci-chemistry/surf |
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+ x11-terms/xterm |
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+ msms? ( sci-chemistry/msms-bin ) |
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+ povray? ( media-gfx/povray ) |
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+" |
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+ |
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+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" |
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+# Binary only plugin!! |
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+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" |
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+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" |
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+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" |
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+ |
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+pkg_nofetch() { |
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+ elog "Please download ${P}.src.tar from" |
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+ elog "${VMD_DOWNLOAD}" |
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+ elog "after agreeing to the license and get" |
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+ elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" |
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+ elog "Place both into your DISTDIR directory" |
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+ elog |
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+ elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" |
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+ elog "file may get downloaded as a compressed tarball or not. In that case" |
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+ elog "you will need to ensure you uncompress the file and rename it" |
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+ elog "as ${P}.src.tar" |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ use cuda && cuda_sanitize |
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+ |
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+ eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch |
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+ |
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+ cd "${WORKDIR}"/plugins || die |
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+ |
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+ eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch |
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+ |
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+ [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) |
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+ |
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+ sed \ |
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+ -e "s:CC = gcc:CC = $(tc-getCC):" \ |
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+ -e "s:CXX = g++:CXX = $(tc-getCXX):" \ |
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+ -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ |
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+ -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ |
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+ -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ |
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+ -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ |
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+ -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ |
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+ -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ |
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+ -e "s:-ltcl8.5:-ltcl:" \ |
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+ -i Make-arch || die "Failed to set up plugins Makefile" |
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+ |
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+ sed \ |
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+ -e '/^AR /s:=:?=:g' \ |
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+ -e '/^RANLIB /s:=:?=:g' \ |
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+ -i ../plugins/*/Makefile || die |
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+ |
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+ tc-export AR RANLIB |
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+ |
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+ sed \ |
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+ -e "s:\$(CXXFLAGS)::g" \ |
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+ -i hesstrans/Makefile || die |
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+ |
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+ # prepare vmd itself |
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+ cd "${S}" || die |
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+ |
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+ eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch |
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+ eapply "${FILESDIR}"/${P}-configure-libtachyon.patch |
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+ |
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+ # PREFIX |
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+ sed \ |
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+ -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ |
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+ -i configure || die |
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+ |
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+ sed \ |
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+ -e "s:gentoo-bindir:${ED}/usr/bin:g" \ |
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+ -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ |
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+ -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ |
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+ -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
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+ -e "s:gentoo-gcc:$(tc-getCC):g" \ |
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+ -e "s:gentoo-g++:$(tc-getCXX):g" \ |
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+ -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ |
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+ -e "s:gentoo-cflags:${CFLAGS}:g" \ |
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+ -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ |
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+ -e "s:gentoo-nvflags::g" \ |
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+ -e "s:gentoo-ldflags:${LDFLAGS}:g" \ |
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+ -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ |
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+ -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ |
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+ -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ |
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+ -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ |
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+ -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
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+ -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ |
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+ -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
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+ -i configure || die |
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+ |
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+ if use cuda; then |
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+ sed \ |
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+ -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ |
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+ -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ |
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+ -i configure src/Makefile || die |
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+ sed \ |
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+ -e '/compute_/d' \ |
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+ -i configure || die |
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+ sed \ |
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+ -e 's:-gencode .*code=sm_..::' \ |
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+ -i src/Makefile || die |
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+ fi |
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+ |
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+ sed \ |
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+ -e "s:LINUXPPC:LINUX:g" \ |
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+ -e "s:LINUXALPHA:LINUX:g" \ |
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+ -e "s:LINUXAMD64:LINUX:g" \ |
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+ -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ |
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+ -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ |
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+ -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ |
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+ -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" |
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+ |
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+ EMAKEOPTS=( |
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+ TCLINC="-I${EPREFIX}/usr/include" |
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+ TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" |
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+ TCLLDFLAGS="-shared" |
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+ NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" |
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+ NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" |
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+ NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" |
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+ NETCDFDYNAMIC=1 |
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+ EXPATINC="-I${EPREFIX}/usr/include" |
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+ EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" |
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+ EXPATLDFLAGS="-shared" |
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+ EXPATDYNAMIC=1 |
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+ ) |
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+ if use gromacs; then |
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+ EMAKEOPTS+=( |
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+ TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" |
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+ TNGINC="-I${EPREFIX}/usr/include" |
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+ TNGLDFLAGS="-shared" |
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+ TNGDYNAMIC=1 |
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+ ) |
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+ fi |
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+ if use sqlite; then |
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+ EMAKEOPTS+=( |
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+ SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" |
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+ SQLITEINC="-I${EPREFIX}/usr/include" |
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+ SQLITELDFLAGS="-shared" |
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+ SQLITEDYNAMIC=1 |
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+ ) |
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+ fi |
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+} |
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+ |
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+src_configure() { |
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+ local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" |
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+ rm -f configure.options && echo $myconf >> configure.options |
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+ |
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+ use cuda && myconf+=" CUDA" |
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+# use mpi && myconf+=" MPI" |
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+ use tachyon && myconf+=" LIBTACHYON" |
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+ use xinerama && myconf+=" XINERAMA" |
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+ |
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+ export \ |
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+ PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ |
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+ PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ |
| 285 |
+ PYTHON_LIBRARY="$(python_get_LIBS)" \ |
| 286 |
+ NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ |
| 287 |
+ NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" |
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+ |
| 289 |
+ perl ./configure LINUX \ |
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+ ${myconf} || die |
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+} |
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+ |
| 293 |
+src_compile() { |
| 294 |
+ # build plugins |
| 295 |
+ cd "${WORKDIR}"/plugins || die |
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+ |
| 297 |
+ emake \ |
| 298 |
+ ${EMAKEOPTS[@]} \ |
| 299 |
+ LINUX |
| 300 |
+ |
| 301 |
+ # build vmd |
| 302 |
+ cd "${S}"/src || die |
| 303 |
+ emake |
| 304 |
+} |
| 305 |
+ |
| 306 |
+src_install() { |
| 307 |
+ # install plugins |
| 308 |
+ cd "${WORKDIR}"/plugins || die |
| 309 |
+ emake \ |
| 310 |
+ PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ |
| 311 |
+ distrib |
| 312 |
+ |
| 313 |
+ # install vmd |
| 314 |
+ cd "${S}"/src || die |
| 315 |
+ emake install |
| 316 |
+ |
| 317 |
+ # install docs |
| 318 |
+ cd "${S}" || die |
| 319 |
+ dodoc Announcement README doc/ig.pdf doc/ug.pdf |
| 320 |
+ |
| 321 |
+ # remove some of the things we don't want and need in |
| 322 |
+ # /usr/lib |
| 323 |
+ cd "${ED}"/usr/$(get_libdir)/vmd || die |
| 324 |
+ rm -fr doc README Announcement LICENSE || \ |
| 325 |
+ die "failed to clean up /usr/lib/vmd directory" |
| 326 |
+ |
| 327 |
+ # adjust path in vmd wrapper |
| 328 |
+ sed \ |
| 329 |
+ -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ |
| 330 |
+ -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ |
| 331 |
+ || die "failed to set up vmd wrapper script" |
| 332 |
+ |
| 333 |
+ # install icon and generate desktop entry |
| 334 |
+ insinto /usr/share/pixmaps |
| 335 |
+ doins "${WORKDIR}"/vmd.png |
| 336 |
+ eprefixify "${WORKDIR}"/vmd.desktop |
| 337 |
+ sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die |
| 338 |
+ domenu "${WORKDIR}"/vmd.desktop |
| 339 |
+} |
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